use of cbit.vcell.math.CSV in project vcell by virtualcell.
the class ReferenceDataPanel method updateReferenceDataFromFile.
/**
* Comment
*/
private void updateReferenceDataFromFile() {
try {
VCFileChooser fileChooser = new VCFileChooser();
fileChooser.setFileSelectionMode(javax.swing.JFileChooser.FILES_ONLY);
fileChooser.setMultiSelectionEnabled(false);
fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_CSV);
// Set the default file filter...
fileChooser.setFileFilter(FileFilters.FILE_FILTER_CSV);
// remove all selector
fileChooser.removeChoosableFileFilter(fileChooser.getAcceptAllFileFilter());
File defaultPath = null;
if (getUserPreferences() != null) {
defaultPath = getUserPreferences().getCurrentDialogPath();
if (defaultPath != null) {
fileChooser.setCurrentDirectory(defaultPath);
}
}
fileChooser.setDialogTitle("Import Data File");
if (fileChooser.showOpenDialog(this) != javax.swing.JFileChooser.APPROVE_OPTION) {
// user didn't choose save
throw UserCancelException.CANCEL_FILE_SELECTION;
} else {
File selectedFile = fileChooser.getSelectedFile();
if (selectedFile == null) {
// no file selected (no name given)
throw UserCancelException.CANCEL_FILE_SELECTION;
} else {
if (getUserPreferences() != null) {
File newPath = selectedFile.getParentFile();
if (!newPath.equals(defaultPath)) {
getUserPreferences().setCurrentDialogPath(newPath);
}
}
CSV csv = new CSV();
RowColumnResultSet rowColumnResultSet = csv.importFrom(new java.io.FileReader(selectedFile));
double[] weights = new double[rowColumnResultSet.getDataColumnCount()];
java.util.Arrays.fill(weights, 1.0);
ReferenceData referenceData = new SimpleReferenceData(rowColumnResultSet, weights);
updateReferenceData(referenceData);
}
}
} catch (UserCancelException e) {
// ignore
} catch (Exception e) {
e.printStackTrace();
if (e instanceof ParseException) {
showHelp((ParseException) e);
} else {
DialogUtils.showErrorDialog(this, e.getMessage(), e);
}
}
}
use of cbit.vcell.math.CSV in project vcell by virtualcell.
the class BrownianDynamicsTest method main.
public static void main(String[] args) {
try {
Options commandOptions = new Options();
Option noiseOption = new Option(OPTION_NOISE, false, "sampled images use Poisson statistics for photons, default is to count particles");
commandOptions.addOption(noiseOption);
Option psfOption = new Option(OPTION_PSF, false, "sampled images are convolve with microscope psf, default is to bin");
commandOptions.addOption(psfOption);
Option imageFileOption = new Option(OPTION_IMAGEFILE, true, "file to store image time series");
imageFileOption.setArgName("filename");
imageFileOption.setValueSeparator('=');
commandOptions.addOption(imageFileOption);
Option plotFileOption = new Option(OPTION_PLOTFILE, true, "file to store CSV time series (reduced data for ROIs)");
plotFileOption.setArgName("filename");
plotFileOption.setValueSeparator('=');
commandOptions.addOption(plotFileOption);
Option displayImageOption = new Option(OPTION_DISPLAY_IMAGE, false, "display image time series");
commandOptions.addOption(displayImageOption);
Option displayPlotOption = new Option(OPTION_DISPLAY_PLOT, false, "display plot of bleach roi");
commandOptions.addOption(displayPlotOption);
Option extentOption = new Option(OPTION_EXTENT, true, "extent of entire domain (default " + DEFAULT_EXTENT_SCALE + ")");
extentOption.setArgName("extent");
extentOption.setValueSeparator('=');
commandOptions.addOption(extentOption);
Option imageSizeOption = new Option(OPTION_IMAGE_SIZE, true, "num pixels in x and y (default " + DEFAULT_IMAGE_SIZE + ")");
imageSizeOption.setArgName("numPixels");
imageSizeOption.setValueSeparator('=');
commandOptions.addOption(imageSizeOption);
Option numParticlesOption = new Option(OPTION_NUM_PARTICLES, true, "num particles (default " + DEFAULT_NUM_PARTICLES + ")");
numParticlesOption.setArgName("num");
numParticlesOption.setValueSeparator('=');
commandOptions.addOption(numParticlesOption);
Option diffusionOption = new Option(OPTION_DIFFUSION, true, "diffusion rate (default " + DEFAULT_DIFFUSION + ")");
diffusionOption.setArgName("rate");
diffusionOption.setValueSeparator('=');
commandOptions.addOption(diffusionOption);
Option bleachRadiusOption = new Option(OPTION_BLEACH_RADIUS, true, "bleach radius (default " + DEFAULT_BLEACH_RADIUS + ")");
bleachRadiusOption.setArgName("radius");
bleachRadiusOption.setValueSeparator('=');
commandOptions.addOption(bleachRadiusOption);
Option psfRadiusOption = new Option(OPTION_PSF_RADIUS, true, "psf radius (default " + DEFAULT_PSF_RADIUS + ")");
psfRadiusOption.setArgName("radius");
psfRadiusOption.setValueSeparator('=');
commandOptions.addOption(psfRadiusOption);
Option bleachDurationOption = new Option(OPTION_BLEACH_DURATION, true, "psf radius (default " + DEFAULT_BLEACH_DURATION + ")");
bleachDurationOption.setArgName("duration");
bleachDurationOption.setValueSeparator('=');
commandOptions.addOption(bleachDurationOption);
Option endTimeOption = new Option(OPTION_ENDTIME, true, "end time (default " + DEFAULT_ENDTIME + ")");
endTimeOption.setArgName("time");
endTimeOption.setValueSeparator('=');
commandOptions.addOption(endTimeOption);
CommandLine cmdLine = null;
try {
Parser parser = new BasicParser();
cmdLine = parser.parse(commandOptions, args);
} catch (ParseException e1) {
e1.printStackTrace();
HelpFormatter hf = new HelpFormatter();
hf.printHelp("BrownianDynamicsTest", commandOptions);
System.exit(2);
}
boolean bNoise = cmdLine.hasOption(OPTION_NOISE);
boolean bConvolve = cmdLine.hasOption(OPTION_PSF);
File imageFile = null;
if (cmdLine.hasOption(OPTION_IMAGEFILE)) {
imageFile = new File(cmdLine.getOptionValue(OPTION_IMAGEFILE));
}
File plotFile = null;
if (cmdLine.hasOption(OPTION_PLOTFILE)) {
plotFile = new File(cmdLine.getOptionValue(OPTION_PLOTFILE));
}
boolean bDisplayImage = cmdLine.hasOption(OPTION_DISPLAY_IMAGE);
boolean bDisplayPlot = cmdLine.hasOption(OPTION_DISPLAY_PLOT);
double extentScale = DEFAULT_EXTENT_SCALE;
if (cmdLine.hasOption(OPTION_EXTENT)) {
extentScale = Double.parseDouble(cmdLine.getOptionValue(OPTION_EXTENT));
}
int imageSize = DEFAULT_IMAGE_SIZE;
if (cmdLine.hasOption(OPTION_IMAGE_SIZE)) {
imageSize = Integer.parseInt(cmdLine.getOptionValue(OPTION_IMAGE_SIZE));
}
int numParticles = DEFAULT_NUM_PARTICLES;
if (cmdLine.hasOption(OPTION_NUM_PARTICLES)) {
numParticles = Integer.parseInt(cmdLine.getOptionValue(OPTION_NUM_PARTICLES));
}
double diffusionRate = DEFAULT_DIFFUSION;
if (cmdLine.hasOption(OPTION_DIFFUSION)) {
diffusionRate = Double.parseDouble(cmdLine.getOptionValue(OPTION_DIFFUSION));
}
double bleachRadius = DEFAULT_BLEACH_RADIUS;
if (cmdLine.hasOption(OPTION_BLEACH_RADIUS)) {
bleachRadius = Double.parseDouble(cmdLine.getOptionValue(OPTION_BLEACH_RADIUS));
}
double psfRadius = DEFAULT_PSF_RADIUS;
if (cmdLine.hasOption(OPTION_PSF_RADIUS)) {
psfRadius = Double.parseDouble(cmdLine.getOptionValue(OPTION_PSF_RADIUS));
}
double bleachDuration = DEFAULT_BLEACH_DURATION;
if (cmdLine.hasOption(OPTION_BLEACH_DURATION)) {
bleachDuration = Double.parseDouble(cmdLine.getOptionValue(OPTION_BLEACH_DURATION));
}
double endTime = DEFAULT_ENDTIME;
if (cmdLine.hasOption(OPTION_ENDTIME)) {
endTime = Double.parseDouble(cmdLine.getOptionValue(OPTION_BLEACH_DURATION));
}
//
// hard coded parameters
//
Origin origin = new Origin(0, 0, 0);
Extent extent = new Extent(extentScale, extentScale, 1);
int numX = imageSize;
int numY = imageSize;
double psfVar = psfRadius * psfRadius;
BrownianDynamicsTest test = new BrownianDynamicsTest();
ImageTimeSeries<UShortImage> rawTimeSeries = test.generateTestData(origin, extent, numX, numY, numParticles, diffusionRate, psfVar, bleachRadius * bleachRadius, bNoise, bConvolve, bleachDuration, endTime);
//
if (imageFile != null) {
new ExportRawTimeSeriesToVFrapOp().exportToVFRAP(imageFile, rawTimeSeries, null);
}
//
if (bDisplayImage) {
new DisplayTimeSeriesOp().displayImageTimeSeries(rawTimeSeries, "time series", null);
}
//
// compute reduced data if needed for plotting or saving.
//
RowColumnResultSet reducedData = null;
if (bDisplayPlot || plotFile != null) {
double muX = origin.getX() + 0.5 * extent.getX();
double muY = origin.getY() + 0.5 * extent.getY();
double sigma = Math.sqrt(psfVar);
NormalizedSampleFunction gaussian = NormalizedSampleFunction.fromGaussian("psf", origin, extent, new ISize(numX, numY, 1), muX, muY, sigma);
reducedData = new GenerateReducedDataOp().generateReducedData(rawTimeSeries, new NormalizedSampleFunction[] { gaussian });
}
//
if (plotFile != null) {
FileOutputStream fos = new FileOutputStream(plotFile);
new CSV().exportTo(fos, reducedData);
}
if (bDisplayPlot) {
new DisplayPlotOp().displayPlot(reducedData, "bleached roi", null);
}
} catch (Exception e) {
e.printStackTrace();
}
}
use of cbit.vcell.math.CSV in project vcell by virtualcell.
the class ImportTimeSeriesFromCSV method compute0.
@Override
protected void compute0(TaskContext context, ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
CSV csv = new CSV();
File inputFile = new File(context.getData(csvFile));
RowColumnResultSet resultSet = csv.importFrom(new FileReader(inputFile));
context.setData(timeSeries, resultSet);
}
use of cbit.vcell.math.CSV in project vcell by virtualcell.
the class ReferenceDataPanel method showEditor.
/**
* Comment
*/
private void showEditor() {
ReferenceData referenceData = fieldParameterEstimationTask.getModelOptimizationSpec().getReferenceData();
if (referenceData != null) {
geteditorTextArea().setText(((SimpleReferenceData) referenceData).getCSV());
} else {
geteditorTextArea().setText("t, data1, data2\n0.0, 0.1, 0.21\n0.1, 0.15, 0.31\n0.2, 0.16, 0.44");
}
geteditorTextArea().setCaretPosition(0);
try {
int retVal = DialogUtils.showComponentOKCancelDialog(this, geteditorPanel(), "time series data editor");
if (retVal == javax.swing.JOptionPane.OK_OPTION) {
RowColumnResultSet rc = (new CSV()).importFrom(new java.io.StringReader(geteditorTextArea().getText()));
double[] weights = new double[rc.getDataColumnCount()];
java.util.Arrays.fill(weights, 1.0);
SimpleReferenceData simpleRefData = new SimpleReferenceData(rc, weights);
updateReferenceData(simpleRefData);
}
} catch (ParseException e) {
e.printStackTrace();
showHelp(e);
} catch (Exception e) {
e.printStackTrace(System.out);
DialogUtils.showErrorDialog(this, e.getMessage(), e);
}
}
use of cbit.vcell.math.CSV in project vcell by virtualcell.
the class KenworthyParticleTest method main.
public static void main(String[] args) {
try {
File baseDir = new File(".");
// File baseDir = new File("/Users/schaff/Documents/workspace/VCell_5.4");
// initialize computing environment
//
File workingDirectory = new File(baseDir, "workingDir");
LocalWorkspace localWorkspace = new LocalWorkspace(workingDirectory);
//
// analyze raw data (from file?) using Keyworthy method.
//
// File vfrapFile = new File(baseDir, "vfrapPaper/rawData/sim3/workflow.txt.save");
File vfrapFile = new File(baseDir, "tryit.vfrap");
ImageTimeSeries<UShortImage> fluorTimeSeriesImages = new ImportRawTimeSeriesFromVFrapOp().importRawTimeSeriesFromVFrap(vfrapFile);
RowColumnResultSet reducedData = new CSV().importFrom(new FileReader(new File(baseDir, "tryit.csv")));
analyzeKeyworthy(fluorTimeSeriesImages, reducedData, localWorkspace);
} catch (Exception e) {
e.printStackTrace(System.out);
}
}
Aggregations